Variant report

Variant	rs56156188
Chromosome Location	chr3:52730699-52730700
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:77)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:77 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr3:52730660-52731130	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:52729652-52730777	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:52728535-52732162	A549	lung:	n/a	n/a
4	POLR2A	chr3:52728377-52732111	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:52729766-52731170	U87	brain:	n/a	n/a
6	POLR2A	chr3:52729809-52732407	U87	brain:	n/a	n/a
7	POLR2A	chr3:52729745-52731974	GM18505	blood:	n/a	n/a
8	POLR2A	chr3:52721385-52732213	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:52729723-52732066	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr3:52728516-52732127	K562	blood:	n/a	n/a
11	NFATC1	chr3:52729822-52732203	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:52729753-52732045	MCF-7	breast:	n/a	n/a
13	POLR2A	chr3:52728456-52732045	GM12892	blood:	n/a	n/a
14	POLR2A	chr3:52728495-52732200	GM12891	blood:	n/a	n/a
15	POLR2A	chr3:52729668-52730710	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr3:52729769-52732167	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr3:52728450-52732180	GM12892	blood:	n/a	n/a
18	PML	chr3:52729706-52731996	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:52729661-52731577	GM12891	blood:	n/a	n/a
20	POLR2A	chr3:52728600-52731923	K562	blood:	n/a	n/a
21	CREB1	chr3:52730559-52731979	GM12878	blood:	n/a	n/a
22	CUX1	chr3:52730339-52731687	GM12878	blood:	n/a	n/a
23	EBF1	chr3:52730655-52731099	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:52728400-52732107	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:52729573-52732032	HUVEC	blood vessel:	n/a	n/a
26	RUNX3	chr3:52730628-52731979	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:52728260-52732231	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr3:52729672-52730990	HL-60	blood:	n/a	n/a
29	POLR2A	chr3:52728520-52732261	K562	blood:	n/a	n/a
30	POLR2A	chr3:52729760-52732251	U87	brain:	n/a	n/a
31	POLR2A	chr3:52728549-52732239	Hela-S3	cervix:	n/a	n/a
32	NFATC1	chr3:52729714-52732265	GM12878	blood:	n/a	n/a
33	HEY1	chr3:52729762-52730738	HepG2	liver:	n/a	n/a
34	RUNX3	chr3:52730505-52731984	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:52728540-52732181	GM12891	blood:	n/a	n/a
36	POLR2A	chr3:52728607-52732171	IMR90	lung:	n/a	n/a
37	POLR2A	chr3:52730201-52730737	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr3:52729701-52730821	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr3:52729671-52730877	H1-hESC	embryonic stem cell:	n/a	n/a
40	FOXM1	chr3:52730416-52731274	GM12878	blood:	n/a	n/a
41	ATF2	chr3:52730577-52731933	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:52729832-52732083	HCT-116	colon:	n/a	n/a
43	POLR2A	chr3:52728311-52732254	H1-hESC	embryonic stem cell:	n/a	n/a
44	STAT5A	chr3:52729651-52732218	GM12878	blood:	n/a	n/a
45	POLR2A	chr3:52728494-52732061	K562	blood:	n/a	n/a
46	MTA3	chr3:52730045-52732023	GM12878	blood:	n/a	n/a
47	PML	chr3:52730653-52731122	GM12878	blood:	n/a	n/a
48	TBL1XR1	chr3:52730614-52731618	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:52728600-52732088	K562	blood:	n/a	n/a
50	POLR2A	chr3:52728559-52732165	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52517647..52519848-chr3:52728042..52731004,2	K562	blood:
2	chr3:52723153..52727199-chr3:52728017..52730930,5	MCF-7	breast:

No data

Variant related genes	Relation type
GLT8D1	TF binding region
ENSG00000212493	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000212452	Chromatin interaction
ENSG00000238862	Chromatin interaction
ENSG00000222345	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10510759	0.83[AFR][1000 genomes]
rs11510435	1.00[EUR][1000 genomes]
rs12107484	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17052357	1.00[EUR][1000 genomes]
rs17052404	1.00[EUR][1000 genomes]
rs1987234	0.84[AFR][1000 genomes]
rs34173244	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35911561	0.87[AFR][1000 genomes]
rs35920544	0.83[AFR][1000 genomes]
rs4532127	1.00[EUR][1000 genomes]
rs56134416	1.00[EUR][1000 genomes]
rs56259931	0.84[AFR][1000 genomes]
rs56276589	1.00[EUR][1000 genomes]
rs56665533	1.00[EUR][1000 genomes]
rs57008939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57246324	0.84[AFR][1000 genomes]
rs57298447	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57319306	0.84[AFR][1000 genomes]
rs57560655	0.84[AFR][1000 genomes]
rs57757646	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57946083	1.00[EUR][1000 genomes]
rs58100002	0.84[AFR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58528592	1.00[EUR][1000 genomes]
rs58564212	1.00[EUR][1000 genomes]
rs58725214	0.84[AFR][1000 genomes]
rs59638016	1.00[EUR][1000 genomes]
rs59869286	1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	1.00[EUR][1000 genomes]
rs60256157	1.00[EUR][1000 genomes]
rs60311166	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60415551	0.84[AFR][1000 genomes]
rs60611300	0.84[AFR][1000 genomes]
rs60682984	0.84[AFR][1000 genomes]
rs60770874	1.00[EUR][1000 genomes]
rs60823713	0.84[AFR][1000 genomes]
rs60830326	1.00[EUR][1000 genomes]
rs60916588	0.84[AFR][1000 genomes]
rs61220667	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61538294	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445536	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762788	1.00[EUR][1000 genomes]
rs6769720	1.00[EUR][1000 genomes]
rs6780005	0.87[EUR][1000 genomes]
rs6780397	1.00[EUR][1000 genomes]
rs72947580	0.84[AFR][1000 genomes]
rs72947589	0.83[AFR][1000 genomes]
rs72950424	1.00[EUR][1000 genomes]
rs72950430	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950432	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950437	1.00[EUR][1000 genomes]
rs72960212	1.00[EUR][1000 genomes]
rs72960237	1.00[EUR][1000 genomes]
rs72960240	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960260	1.00[EUR][1000 genomes]
rs72960274	1.00[EUR][1000 genomes]
rs72960281	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960285	1.00[EUR][1000 genomes]
rs72965177	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72965181	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73839126	1.00[EUR][1000 genomes]
rs73839129	1.00[EUR][1000 genomes]
rs7619643	0.85[AMR][1000 genomes]
rs7645785	1.00[EUR][1000 genomes]
rs764636	1.00[EUR][1000 genomes]
rs7647992	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7648016	0.81[AFR][1000 genomes]
rs934839	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52721000-52734400	Strong transcription	Fetal Stomach	stomach
2	chr3:52721000-52738600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:52721200-52731600	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr3:52721200-52732200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:52721200-52732200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr3:52721200-52732200	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:52721200-52733000	Strong transcription	Stomach Smooth Muscle	stomach
8	chr3:52721200-52734400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr3:52721400-52730800	Strong transcription	Lung	lung
10	chr3:52721400-52731800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:52721400-52732000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:52721400-52732200	Strong transcription	Brain Angular Gyrus	brain
13	chr3:52721400-52732200	Strong transcription	Colon Smooth Muscle	Colon
14	chr3:52721400-52732400	Strong transcription	Brain Anterior Caudate	brain
15	chr3:52721400-52732400	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:52721400-52732800	Strong transcription	Fetal Brain Female	brain
17	chr3:52721400-52732800	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:52721400-52733000	Strong transcription	Adipose Nuclei	Adipose
19	chr3:52721400-52734000	Strong transcription	Primary B cells from cord blood	blood
20	chr3:52721400-52734200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:52721400-52734400	Strong transcription	Brain Hippocampus Middle	brain
22	chr3:52721400-52734400	Strong transcription	Fetal Lung	lung
23	chr3:52721400-52734400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr3:52721400-52734600	Strong transcription	Primary T cells from cord blood	blood
25	chr3:52721400-52735800	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:52721600-52730800	Strong transcription	Spleen	Spleen
27	chr3:52721600-52731200	Strong transcription	HSMMtube	muscle
28	chr3:52721600-52732000	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr3:52721600-52732000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:52721600-52732000	Strong transcription	Brain Cingulate Gyrus	brain
31	chr3:52721600-52732000	Strong transcription	Left Ventricle	heart
32	chr3:52721600-52732000	Strong transcription	Ovary	ovary
33	chr3:52721600-52732000	Strong transcription	Right Ventricle	heart
34	chr3:52721600-52732200	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:52721600-52732400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:52721600-52732400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:52721600-52733600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:52721600-52734200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:52721600-52734200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:52721600-52734400	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr3:52721600-52734400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:52721600-52734400	Strong transcription	Thymus	Thymus
43	chr3:52721800-52731200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr3:52721800-52731200	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr3:52721800-52732200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:52721800-52732400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:52721800-52732400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:52721800-52732400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:52721800-52733000	Strong transcription	Placenta	Placenta
50	chr3:52721800-52734400	Strong transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links